Lee was educated in Taiwan and at the University of California at Berkeley (Ph.D., 1965). He did postdoctoral work at Harvard University and Berkeley and then taught at the University of Chicago from 1968 to 1974. He became a U.S. citizen in 1974 and moved from Chicago to Berkeley, where he continued his research.

As a postdoctoral researcher, Lee experimented with and further developed Herschbach’s invention of the “crossed molecular beam technique”—a technique (derived from elementary particle physics) in which beams of molecules are brought together at supersonic speeds under controlled conditions to allow detailed observation of the events that occur during chemical reactions. Lee extended Herschbach’s technique, introducing mass spectroscopy to identify the products resulting from the reactions of oxygen and fluorine atoms with complex organic compounds.